Not Just Friends
by AndromedaMarine
Summary: The first tragedies they all dealt with informed and reminded every member of the expedition that their presence there did not come without inevitable losses and unending casualties. COMPLETE.
1. The First Tragedies

**Not Just Friends by AndromedaMarine**

_The First Tragedies_

One year passed and Peter Grodin died. Two years passed and who-knows how many soldiers died during the siege. Three years passed and Carson Beckett died. Four years passed and Elizabeth Sheppard died, leaving her husband to care for their two daughters. John still had Rodney, Teyla and Ronon as his team; Lorne somehow managed to strike up a relationship with Laura Cadman and now they were engaged. Rodney and Jennifer Keller were getting closer each day and the two off-worlders had been together for a long time.

Realizing that Atlantis was an actual city and not just an expedition anymore General Hank Landry revised regulations allowing marriages and children. His first clue was the birth of twins Antissa and Nara Sheppard. His second clue was the birth of Torren John Emmagan not long after the Sheppard kids were born. Antissa and Nara were five months when their mother died. It tore John apart to lose his leader – even more so to lose his wife and mother of his children. From that day forward he was more careful than usual on missions – he made sure that every time he went through the gate he'd be coming back.

Things just weren't the same with Sam Carter as their leader – she didn't have the same diplomatic skills that Elizabeth had possessed, although her experience with the Stargate outranked everyone, even Rodney. John knew that one day, quite soon, he would have to choose another Atlantean couple as his children's godparents. In reality if he died Antissa and Nara would be under the protection of the city, but everyone needed parents.

When Rodney and Jennifer married John had his answer. The newlyweds had given the Colonel a heartfelt 'yes' and decided to spend their honeymoon on New Athos. They were gone for one week when they got word that Radek had been seriously injured while working on an Ancient device. Rodney insisted that they return at once – to give moral support and so he could figure out what went wrong with the device.

Jennifer tended to Radek, who had massive burns on over half his body. It was a miracle he lived, she had said. Rodney told Radek to be more careful, and began to watch out for John on missions. It was now nearing the end of their fifth year on Atlantis and Rodney was dreading the day when someone he knew, cared about and loved died. It had become a pattern that was heart-wrenching and painful every year when the inevitable approached. Neither John nor Rodney could keep their emotions in check for long. It could be either one – John or Rodney, maybe Evan, or even Chuck Campbell. Perhaps this time it would be Jennifer, or Katie. God forbid Sam die, leaving their city once again leaderless. Or maybe Radek. Ronon, or Teyla? John couldn't stand it.

The first tragedies they all dealt with, the group of mourners at the time including Carson and Elizabeth, informed and reminded every member of the expedition that their presence there did not come without inevitable losses and unending casualties. The first tragedy for Antissa and Nara was the death of their mother. Their second tragedy was approaching.


	2. Five Years Gone

**Not Just Friends by AndromedaMarine**

_Five Years Gone_

It had come. The inevitable period of time where someone was bound to die came – and went. Not surprisingly, it took lives from the Ancient city with it, although causing shock for everyone who knew the two who were taken. Everyone had expected them to live, to be the strongest and the ones that lived out their lives on the Great City. Two caskets, one bearing the American flag and one bearing the flag of the Czech Republic were slowly taken through the Stargate back to Earth. Everyone was crying, no one could bear to hold it in, not even Sam. Sam had remained alive, which was a blessing in itself. But two brilliant, two brave, two heroic men were gone forever. Five years gone and so were the two men Evan Lorne and Rodney McKay had called dear friends.

Jennifer McKay could not bear to watch as her husband took John Sheppard and Radek Zelenka back to Earth. Laura Lorne as well couldn't stand it. Both had their eyes closed and both held on to the children left in their care. Antissa and Nara were still too young to understand what had happened to their father. They would never really know their biological family, as Jennifer and Rodney were legal guardians to the twins.

John Sheppard had lived life not full enough; he still had fight and a future left in him when he was shot in the back by the Genii. Rodney couldn't help but feel responsible for both the scientist's and the colonel's deaths as Radek had taken Rodney's place on that particular mission. The ceremony reminded him painfully of the weight he had to bear returning Carson's body to the Highlands. At that time Carson Beckett had been the closest thing to a best friend he'd ever had. Now the two men, who were not just friends – they were family – were gone, along with the five years for which he had known them both. He couldn't be strong, not this time. He couldn't hold the tears in as he did for Carson's memorial. The pain of losing John and Radek was just too great, even for this tough scientist. As he, Ronon, Lorne, Chuck, Teyla, some botanists, and four marines slowly passed into the event horizon, Rodney cried. This was it – he couldn't take any more. He would never leave Atlantis, no, but at the moment these two losses broke him like no other had before.

Antissa and Nara were in Jennifer's and Laura's arms as the funeral procession left. Samantha stood solemnly beside them, her head down and her cheeks streaked with tears shed over John's death. She had loved him as a friend and as a leader; she hadn't imagined losing two of her best in duty.

Atlantis wasn't full of friends. They were more than that – the city was a family. And with that family came the responsibility for Rodney and Jennifer to raise and introduce Antissa and Nara Sheppard to the world of Atlantea and the Pegasus Galaxy. They would be the oldest and firstborn children of the Tau'ri to ever live their whole lives on Atlantis.

The one-year-old twins had no understanding of their second tragedy, or even of their first. But in later years the stories told them that their parents were heroes in more than one interpretation of the word.


	3. Unbroken Family

**Not Just Friends by AndromedaMarine**

_Unbroken Family_

When the twins were one and a half they began to talk and their first words, respectively between Antissa and Nara, were 'dada' and 'mama.' At this event Rodney could not help but shed tears; after all it was only six months after their true father's passing. Jennifer had showed considerably less emotion, although in reality she waited until she was entirely alone to cry. Not long after John had died the McKays' had given birth to a boy, whom they decided to name John Carson McKay in honor of the fallen CMO and colonel. John Carson (being one year younger than the twins) adored and looked up to his sisters. Even after learning that they weren't related to him by blood his feelings didn't change.

Three years after John and Radek died was another siege. This time the Wraith were fended off by Rodney's brilliant idea to place the twins in the chair, which caused a new (well not so new to the city) power source to activate and blasted the hive ships out of the sky. Nara and Antissa, four years old at the time, didn't really know what they were doing as they sat in the glowing blue chair. Afterwards the twins were praised by everyone on base and Sam had to take extra precautions so the twins weren't overwhelmed. True to their sibling type they looked exactly alike except for their birthmarks. While in the exact same spot, they had distinct differences. Antissa's birthmark, on her neck, was shaped rather like a heart, and Nara's looked like a quarter moon. This way the McKays' could distinguish their adoptive children.

On the twins' fifth birthday there was a big party held in the mess hall. By that time Samantha Carter had been removed from command and now Cameron Mitchell and Daniel and Vala Jackson were permanently retired from the SGC and living on Atlantis. By no means were they retired from missions through the gate; they simply had enough of the IOA interfering with the Milky Way's problems. Besides, Atlantis needed an archaeologist who was fluent in Ancient and a new leader – Cameron. Vala was very pregnant with the Jacksons' second child – the first, a girl named Halajier, being five years old as well – when they attended Antissa's and Nara's birthday party.

Hala and the twins were friends and would grow to be like true sisters. The whole of Atlantis acted as the family it was. The Lornes' son, Donovan, was John Carson's age and subsequently became best friends. By the twins' sixth year of life Ronon and Teyla had another child besides Torren, a girl named Mary in memory of John's favorite football play (the Hail Mary). Vala and Daniel's second child, a boy they named Benjamin, became Mary's playmate and best friend.

The whole of Atlantis became more intertwined than anyone could've thought possible. Its children and eventually grandchildren was a city of not just friends.

The city was a family fathered by the Sheppards, for without the birth of their twins no initiative would have taken place to make Atlantis a real city.

Of course, many more people died every year as was pattern. But The Family itself remained unbroken.


	4. The First Flashbacks

**Not Just Friends by AndromedaMarine**

**Author's Note: minor/moderate spoilers for the episode: Sateda (3x4)**

_The First Flashbacks_

"_Rodney, cut it out. I can't concentrate when you're doing that," Carson berated as the scientist began to protest and squirm. Only while under the effect of morphine would Rodney allow the Scot to work. The arrow still jutted precariously and conspicuously from his ass, and the Head of Sciences couldn't help but object._

"_I'm sorry, Dr. Voodoo, but it HURTS!" Rodney tried to tug the oxygen tube from his nose._

"_Aye, I'm aware of that, lad, but it's necessary. You can't very well sit on an arrow." Sighing, Carson injected a rather large amount of morphine into Rodney's IV. Immediately the scientist relaxed and drifted off. Elizabeth walked in._

"_All the colors. All the pretty horses," Rodney said, the oxygen tube successfully re-stuffed into his nose and his ass covered with surgical plastic. _

"_What's he talking about?" Elizabeth Weir asked, eyebrows rising to their full height. She put her hands on her hips and cocked her head at the scientist. _

"_I gave him some morphine for the pain," Carson explained, half frowning and half smiling. "Perhaps a wee bit much. He was making it impossible for me to work."_

_An air force major leaned over the table, accentuating his words as to catch Rodney's half-witted attention. "I need to know how many villagers there are. How far is the village from the gate? What kind of weapons do they have?"_

"_I'd bet something that shoots arrows," Carson said, gesturing to the arrow that was still sticking obviously out of Rodney's ass. _

"_Excuse me," Rodney asked, blinking up at the major. "Have you seen a guy? He looks like you but he's got messy hair. I think I lost him. Oh, and a pretty woman and a caveman?" The major rolled his eyes and left the infirmary to gather a rescue team. "Excuse me," Rodney said again, trying to shift – Carson's hand pressed firmly down on Rodney's back, immobilizing him. "Why am I lying here?"_

"_You have an arrow, Rodney, in your gluteus maximus!" Carson said, pronouncing each word clearly to penetrate the morphine veil. _

"_Oh, that sounds painful," Rodney said, letting his head fall back onto the table. "Gluteus maximus," he mumbled. "Oh my god! That's my ass, isn't it?"_

"_Aye," Carson replied, sighing heavily._

"_Call me if he makes any sense," Elizabeth said, and left the room._

Rodney sat up in his bed beside a sleeping Jennifer. It had been several years since he'd had a flashback – except this one involved three of the people he was most close to. Carson, Elizabeth and a mention of John – it was painful, and not from the scar that was still residing on his butt. He wrapped an arm around Jennifer and fell back asleep, a small smile gracing his face. Although the sadness was great, the memory was a happy one – one whose outcome had been successful.

--

_The call had come from Lt. Colonel Cameron Mitchell. She'd heard of and seen him before, having been involved with Stargate Command and working with Dr. Lam for a few months. But these circumstances were much different. They scared her. "General Landry and I need to speak with you," he had said. Ominous? Perhaps. Frightening? Definitely. _

_She knocked on the door to Landry's office. The door opened, revealing Mitchell, General Landry, and three men she didn't recognize. "Dr. Keller, this is Colonel Sheppard, Dr. McKay and Ronon Dex. I'm afraid the circumstances are far from perfect."_

"_Sir?"_

"_You're being promoted, Doc," Cameron said, running a hand through his short brown hair. _

_The one called Rodney had puffy red eyes and John had an expression that was past sadness. "You remember Dr. Beckett, right?" John said. _

_Jennifer Keller nodded. "Yeah, I know his work. He's quite gifted."_

_Rodney sniffed._

"_I'm afraid there's been...oh, God how do I put this...there's been an accident. An explosion. He's – Carson's – he's gone," John said quietly. Rodney couldn't bear to look anymore and closed his eyes. It was obvious he had been very close to Carson._

_Jennifer covered her mouth. "Oh my God. That's...that's horrible."_

"_You'll accompany these men back to Atlantis in two days. Dr. Keller, do you have any family on Earth?"_

"_None that I still keep in touch with," she replied, still trying to comprehend the shockwave still battering her. "I'll be ready, sir. Don't worry." Before she left she went up to Rodney. "I'm so sorry, Dr. McKay. Dr. Beckett was a brilliant and caring man. Were you close?" she rested a hand on his arm._

"_Like brothers," Rodney said, barely audible. "Thanks."_

_Jennifer Keller left the room, not knowing that her simple act of kindness began the relationship between herself and the grieving scientist. She left the room knowing that she was replacing, in her opinion, the most brilliant and most skilled xenobiologist and medical doctor in the world, which she was._

Jennifer knew it had been a dream when she awoke. Remembering the circumstances which brought her to Atlantis nearly killed her again. Although she didn't personally know Carson or even have the honor of meeting him she understood and respected the family he'd left behind on Atlantis.

Those flashbacks were only the beginning for those closest to the Sheppards and Carson.


	5. The Heart of Atlantis

**Not Just Friends by AndromedaMarine**

_The Heart of Atlantis_

Rodney, the next morning, couldn't help but think upon the night before as a reminder of who his family was. He was not only one with the universe, he was one with Atlantis. As his wife slept next to him, peacefully enjoying the morning air, the doctor of sciences looked upon his past with new recognition. Over the years, his family had strengthened, not fallen apart, and as to deny the popular belief that the beheld most of Atlantis, John was more than a brother. It almost seemed as it couldn't be so. He knew that one day in the future, soon, if not entirely immediate, he would lose his family and have to walk the bleary path presented him alone.

Most of the expedition members looked on Rodney has a particular type of leader. He had the brains needed and the required willpower to take on any problem presented him. But this, this was different. Oh, how different it was to have people stare at you just for the reason you are one of the first. Generations were beginning to pass and before he knew it Rodney's mind was seemingly no longer the smartest in three galaxies, even though it was. Of course, his colleagues and esteemed friends always looked on him as the one who saved them more than once from terrible disaster, and if no one else was going to recognize it, they would.

Antissa and Nara Sheppard would always keep their father's name, but their true family was with John Carson, Jennifer and Rodney. Their true family was Atlantis.

While in their early teens the two twins became, as normal, interested (if the feeling could be called such) in the opposite sex. The McKays, with Rodney being the nitwit that he is, had a rather difficult time talking to their children (all four, the youngest being Scott) about the subject.

During the times he needed help raising the two children Sheppard had left him Rodney McKay found comfort and solace in the flashbacks that told Sheppard's true nature. John had loved and cared for his children, there was no doubt about that, but Rodney couldn't help but sometimes think that John had meant for it to happen. After such thoughts flowed into Rodney's mind more than once the good Canadian – the Atlantean – found himself wishing there'd only been more time, more time to save him. Jennifer had done her best to save John. But for Rodney the saddest thing was Radek had no chance – he died instantly.

--

_He didn't talk to anyone for days, maybe weeks. Everyone who tried to get close to him, to comfort him, was pushed violently away. Everyone except his wife and John's now-fatherless daughters. He acknowledged them, perhaps spoke – if minimally – to them, but he never spoke about it. It was too painful, too much, and just not fair. It should have been him. He should have been the one carried back to earth, not John. Not Radek. Him. _

_He couldn't help but blame himself – he'd insisted on staying back on base for that mission because of the new Ancient device that apparently had its own power source that was greater than three ZPMs combined. It later proved to be the necessary weapon to bring the Wraith to their knees during the second siege. No amount of sympathy or attempted persuasion toward the fact that it wasn't his fault gave him comfort. He couldn't and never would forgive himself. _

_Even when Sam granted him a week's vacation he found himself perpetually in his lab. With no Radek there to defiantly point at the door he spent days alone. Sometimes he would forget meals, something that never happened when Carson or John was alive. Both would make sure that the doctor ate during the course of the day. Miko wasn't as persistent when attempting to get Rodney to eat and eventually her time to die came as well._

_If not for Jennifer, the twins and his son Rodney would have fallen into an oblivion no one but his family could rescue him from. John had been his family. Radek had been his family. Carson had been his family. But because of Jennifer's kindness after Carson's death the oblivion was not a permanent solution. _

_Eventually the sadness of loneliness caught up to Rodney and once more he sought and found refuge with his family. Everyone understood how he felt. But no one was more distraught than the scientist that had looked out for John, the scientist who had become John's brother, the scientist who blamed himself, the scientist who failed to adhere to his one, simple rule: keep John alive._

--

Now finding it force of habit to give in to a child's request the man had to learn. Before, when John and Radek were alive, the scientist loathed and despised any human being under the age of sixteen simply because of their whiney dispositions. Pregnancy had been good to the McKays. Rodney was now the most placid and loving father on Atlantis. Even Evan Lorne couldn't measure up to the usually arrogant and bitter doctor.

Rodney had found the metaphorically open door and he was about to walk into it. He was one of the few-remaining first. John, Elizabeth, Carson and Radek were all gone, never to return and re-claim Atlantis with him. But their children lived on. Of the eight or so people Rodney became friends with during the first year on Atlantis, only three were still alive. And Rodney would be the only one, the true scholar and survivor in the fight of the universe, the only one to survive. He would meet so many people and watch the same die in the war.

In a midnight revelation many years after his children grew, Rodney saw the true meaning of family. Family wasn't who was related to whom by which means. Family meant caring for each other and saving each other's lives. Family meant available comfort at all hours no matter what was bothering you. Family meant he'd be there if something went wrong. Family meant he'd save them a million more times if it meant he'd get to see his sons and daughters again.

For Rodney, Atlantis was a part of his family; Atlantis cared for and looked after him and his children like no one else would. Atlantis had a heart.

So, four families, each serving as a representative of the individual team member, became legend on Atlantis. The Sheppards, called the founders. The Lornes, called the guardians. The Dexes, called the warriors, and the McKays, called the heart of Atlantis.


	6. Epilogue

**Not Just Friends by AndromedaMarine**

_Epilogue: 73 Years Later_

"Our father would have been proud."

"He is proud. He's here, Nara. He's always been here. I keep forgetting that we're not really related."

The old woman gave her brother a kiss on the cheek and hugged him. "Scott, we'll always be related. Our true fathers were brothers, remember? But Rodney raised us. He raised Antissa and me as family. No one can take that away from us."

"I'm sorry for your loss, Nara."

A tear glistened on her cheek. "Donovan was strong through the end. I'm just relieved that he lived through all the dangerous missions his father didn't. He didn't suffer, Scott. He chose to live on with the Ancients." She leaned against the railing. "You know what's strange?"

Scott glanced at his sister. "What?"

"The earliest thing I remember about life is my mother."

"Jennifer?"

Nara shook her head. "No. Elizabeth Sheppard."

Scott's eyebrow rose. "You were five months old. That's amazing."

Nara sighed. "I know. I still can't believe that Dad's gone."

"One hundred and six is an old age to live to, even by Earthly standards."

Nara shrugged. "I don't think so, not anymore. The advances that Mom and Dad made with medicine and science far outrank any other earthly doctor. They both could have lived longer."

"He made the choice to ascend, Nara. But he lived a full life. He saw children, grandchildren and great-grandchildren. He even saw the Stargate Program go public." Scott rested a hand on his sister's and sighed. "He saw the Wraith eradicated."

Nara smiled. "What a feat. But now we have the Dinarai to deal with."

"Don't worry about them. Our children will handle this threat."

The older sibling was silent for a long while. "Do you realize that no new personnel from Earth have been brought here since 2029? Atlantis has been a true city. Recreating and replacing those lost in the wars. She's a city again, Scott."

After another few minutes Scott McKay spoke. "Elizabeth's waiting for us. We should get going." The two siblings left the Balcony of Sanctity and joined Nara's daughter, Elizabeth, and her family. Over the years the McKays, the Lornes, the Dexes and the Jacksons had become intertwined and intermarried. Everyone was related to everyone whether they liked it or not.

--

"_Antissa, Nara, happy seventeenth birthday," Rodney said, handing each of his daughters a small, wrapped package. "Open them." He smiled and took Jennifer in his arms, smiling as the twins excitedly opened the gifts. _

"_What is it?" Nara asked, staring intently at the small, rectangular piece of metal. "It looks like what Evan wears."_

_Jennifer took a deep breath. "Those were your father's."_

_Antissa was confused. "Dad's not military."_

"_I know we should have given them to you much earlier, and I'm sorry we didn't," Jennifer said. "They were John Sheppard's."_

_Neither twin said anything. They had heard the stories of their father's death – some of which were grossly disproportioned and wildly inaccurate. But for the most part they knew that both their real parents were heroes. _

_Moving on, Rodney said, "You both also have permission to take the Jumpers out whenever you like, except when they're required for missions. Next year you can officially be on one of the teams." He took his daughters into a loving embrace. "Keep them close to your hearts – John would have wanted that."_

--

Rodney McKay was the only one out of himself, John, Ronon, Teyla or Evan to see the wraith eradicated. Rodney was the true survivor. He was respected and admired on Atlantis, and for a short period, even got to command the city. Following the footsteps of Elizabeth, Sam and Cameron had been an honor that Rodney never boasted of. He went from being the arrogant, petty and brash man to the humble, understanding, loving and fighting heart of Atlantis.

So the generations continued. The Great City would be called home by the descendants of the Earthlings until Atlantea's sun died. Nara and Antissa Sheppard both lived to be one hundred and thirty four years old. The advancements their parents had made helped them a great deal. They lived to see the threats of the Wraith and Dinarai wiped out. Both ascended, following the footsteps of those Atlantis cared for: Elizabeth Sheppard, Rodney McKay, Jennifer McKay, Donovan Lorne, Elizabeth Jennifer Lorne, Evan Lorne, Laura Lorne, Teyla Dex, Halajier Jackson, Daniel Jackson (his third and last time), Vala Jackson, Mary Dex, John Carson McKay, Benjamin Jackson, Scott McKay, and John Sheppard.

No, the Sheppards, McKays, and Lornes never died. The founders, guardians and heart of Atlantis would always live, together, in harmony.

Atlantis, in essence, had ascended.

And the Family remained unbroken.


End file.
